A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

Nat Commun. 2018 Apr 13;9(1):1444. doi: 10.1038/s41467-018-03614-0.


The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here we test the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~ 15 CTCF binding sites and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-specific or allele-specific manner. In contrast, Firre's deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms may play roles in establishing TAD boundary formation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor / chemistry*
  • CCCTC-Binding Factor / genetics
  • Chromatin / chemistry
  • Chromosomes, Human, X*
  • DNA, Complementary / metabolism
  • Female
  • Gene Deletion*
  • Gene Library
  • Genome, Human
  • Humans
  • K562 Cells
  • Male
  • Mice
  • Mice, Knockout
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Domains
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • Repressor Proteins / metabolism
  • Sequence Deletion
  • Transcription, Genetic
  • X Chromosome
  • X Chromosome Inactivation*


  • CCCTC-Binding Factor
  • CTCF protein, human
  • Chromatin
  • Ctcf protein, mouse
  • DNA, Complementary
  • Firre long non coding RNA, mouse
  • RNA, Long Noncoding
  • Repressor Proteins
  • long noncoding RNA Firre, human